I just don't find it plausible that the ship would look brand new after all the battles it's fought and all it's gone through. It should be bruised and scarred (both the interior and the exterior) and supplies should be running out.

In Farscape, Moya goes through nasty stuff and it never changes or shows battle damage. Only once in the entire show do they have to take it to a specialist for repair work.

The crew should be down in the dumps and depressed. After all, all of their opportunities to get home have been foiled by their very own captain.

Deep-Space missions are supposed to last for years (Kirk's was 5 years) away from home and out of touch with Mission Control. And both Kirk and Picard have been in their same situations and yet both managed to return home okay. No reason to get that depressed when at least 5 years away from home is what they signed on for, and they know that this isn't some impossible situation.

A fight for control of the ship would be realistic, especially considering that the Maquis aren't as disciplined and principled as the Starfleet officers.

Agreed, but the Fleeters outnumber them 3-1 if not more.

I could easily see Maquis murdering Starfleet officers in their sleep.

This, not so much. Why would the Maquis do this? They weren't hardcore arch-enemies of the Feds, their enemies were the Cardassians. They didn't even have really serious differences with the Feds in terms of how they operated, since their own leader was an Ex-Fleeter who brought most of his experience to them.

This would also be a great opportunity to examine the Starfleet officers; how do they respond to the Maquis threat? Do they negotiate and make peace with the Maquis like they have been trained to do, or do they throw their principles aside and fight for their life?

But the Maquis and Feds weren't really enemies in the first place, and the local Maquis Leader (Chakotay) WAS an Ex-Fleeter.

He wasn't even a traitor like Eddington, he formally resigned and THEN joined the Maquis, and he didn't betray secrets or operations in the process. Or go out of his way to antagonize the Feds.

If anything, Chakotay would've been one of the first ones to just say "Look people, we're stuck out here through no fault of anyone. These guys are willing to let bygones be bygones, and frankly they're the only thing we have in the DQ close to a friendly face. We can either work together to try and survive, or we can just ask them to drop us off on the next commerce world, and I'd rather we all stayed here on an advanced Starship."

Yes, this should have all been addressed in the show itself but the bottom line is that the Maquis were never going to be truly adversarial to the Feds and whatever tensions between them would realistically be resolved in 1-2 seasons. Any more than that is just crazy.